Hi, my name is Brandon Zhang and I'm 15 years old. I'm from Winchester, MA, a small suburb of Boston and I'll be going into 10th grade. I've just finished the beginning chapter of my high school career and look forward to how my knowledge and studies can expand as I travel through high school. Ever since biology was introduced to me in the beginning of my freshmen year, I have always loved it. To this day, it has been my favorite subject in science and I've been particularly interested in biotechnology, microorganisms, and anatomy and physiology.
Even though I like traveling and have visited many different cities across the world, I have lived in the Boston area all my life and have been grateful for fifteen years for living in one of the biggest science centers in the United States. The atmosphere that I have been able to be surrounded in is just incredible. The amount of technology being developed here as a result of research in the different fields of science has always amazed me. In addition, the fact that both my parents have worked at Massachusetts General Hospital, one of the top hospitals in the nation for a long time, has piqued my interest in the field of biotechnology and anatomy and physiology. Both my mother and my father has manipulated bacteria and viruses to try to help in the fight with various diseases.
When I am not reading biology articles or thinking about bacteria, I enjoy playing tennis on my high school's varsity team and solving competitive math problems, hobbies of mine since sixth grade. I also have been playing piano for eleven years (I especially love Chopin) and saxophone for four years. Even though getting a concussion from sailing was a painful experience, it was actually a fun one for me because I got to learn a lot about how the brain works and how to protect it in the future.
Just like the elegant proofs to many math problems I have solved over my competitive math career, the beautiful solutions to many real world problems biologist come up has never ceased to amaze me. I would have never of thought of to use electrical currents to separate different lengths of DNA or that DNA comes in a double helix shape with certain rules on how nucleotides pair up. In the mathematics field, you can't just prove the Cauchy-Schwarz inequality when you just get started, but over several weeks, you can develop your skill and knowledge - and that's why I am here at BLI, to develop and improve my biology experimental skills and knowledge of real life problems.
I am looking forward to perform experiments, research on current biology topics and problems, and learn as much as I can about biology at Boston Leadership Institute.
The Problem:Even though bacteria are microscopic, how are they able to create so much trouble in hosts that are one million times their size? It turns out that bacteria are able to communicate with each other through a method called quorum sensing. With quorum sensing, the bacteria are able to sense how many other bacteria of the same species are in the area. When the concentration of a species reaches a threshold, they can all perform an action simultaneously that will achieve a big task. Virulent bacteria uses this method to talk and organize a gang attack to cause a disruptence in the host organism. With the increased use of antibiotics used to fight off infections, bacteria are starting to evolve to be resistant to antibiotics.
History of Quorum Sensing Discoveries:In the late 1960’s, J Woodland Hastings and Kenneth Nealson were studying Vibrio Fischeri, a bacteria that is able to produce light. They realized that the bacteria glows only when high concentrations of them are present. At first, it was believed that in the lower densities of bacteria, there was an inhibitor that prevented light production. However, they eventually realized light production was because of an activator molecule. In 1981, the autoinducer in Vibrio fischeri was discovered by Eberhard. In the early 1990’s, Barrie Bycroft and Paul Williams realized that quorum sensing is not only limited to marine bioluminescent bacteria and that virulent bacterial species use quorum sensing. In 1993, the first biosensers that can detect AHL (an autoinducer that will be discussed later) were developed. Now in modern times, Bonnie Bassler discovered the autoinducer for interspecies communication as well as some molecules that can inhibit quorum sensing and with ideas about if quorum sensing is the link between unicellular organisms and multi-cellular organisms. .
Quorum Sensing in a Nutshell: Bacteria can communicate through quorum sensing by releasing a small protein called an autoinducer. When the autoinducers bind to receptors on the cell membrane the receptors, the bacteria will start producing autoinducers. When these autoinducers reach a certain threshold, the receptors will alter the gene expression directly or indirectly. These receptors directly alters the gene by acting as an activator or repressor to turn genes on or off in gram negative bacteria. They alter the gene indirectly by allowing response regulators to send signals downstream to transcription factors to turn the gene on or off in gram positive bacteria. The altered gene allows bacteria to know that they are in a densely populated area of bacteria and will perform a task that can only be achieved when many bacteria are in the area. By being able to perform quorum sensing, bacteria can maximize its energy output to perform large tasks.
Different types of Quorum Sensing: Bacteria can be classified into two categories based on their cell wall. If bacteria had a thick layer of peptidoglycan in its cell wall, it is classified as gram positive. If bacteria had a thin layer of peptidoglycan in its cell wall, it is classified as gram negative. In gram negative bacteria, quorum sensing is done through three components, the I synthase protein used to make autoinducers, the N-acyl homoserine lactone (AHL) autoinducer, and the R receptor proteins, which are DNA binding transcription factor. AHLs are small neutral lipid molecules made up of a homoserine ring and an acyl chain. The acyl chain is what distinguishes between different types of gram negative bacteria. In gram positive bacteria, quorum sensing is done through a two component signaling system and some response regulators downstream. The two component signaling transduction system uses autoinducing peptides (AIP) as autoinducers and specific histidine kinase receptors that will phosphorylate downstream adaptor proteins once bound. AIPs are different from AHLs because they require cell surface oligopeptides transporters to help AIP secretion into the environment and they are peptides compared to lipids . Below will be a more in depth analysis of quorum sensing in gram negative bacteria versus gram positive bacteria.
Solution: With all the antibiotics being used to fight off infections, targeted bacteria are going to evolve because of the selective pressure of the antibiotics. For quorum sensing to work, all parts of the system have to work. That means scientists can target one of the parts in the quorum sensing system to disable quorum sensing regulated genes and not allow bacteria to express virulence factors. This is known as quorum quenching. Because bacteria usually attacks with its own species and not with others, most of the following solutions will focus on intraspecies communication.
In Gram Negative Bacteria:The most well known quorum sensing system is with the LuxR/LuxI proteins, the autoinducer receptor and autoinducer synthase respectively. Although there are other known quorum sensing systems in gram negative bacteria, the bulk of research has gone into this LuxR/LuxI system and how to interfere with it. When the AHL concentration gets high, they will bind to the LuxR type proteins causing the receptor to alter the quorum sensing targeted genes and allow the LuxI type synthase to create more of the AHL autoinducer. Without AHL binding to LuxR, LuxR will degrade to prevent bacteria from short circuiting their quorum sensing systems.
Disabling the autoinducer: In gram negative bacteria, biologists are able to disrupt the autoinducers by breaking down the signal molecules. This is done when enzymes such as acylase, lactonase, and oxidoreductases use hydrolysis to break apart AHL autoinducers. These enzymes have been isolated from several bacteria species such as Streptomyces and Deinococcus. In addition, biologists working with Vibrio fischeri have noticed that silicon dioxide with β-cyclodextrin binds to AHL and then removes the autoinducers from the immediate environment, but this has not been tested yet on autoinducers of other gram negative bacteria
Blocking the Receptor: In gram negative bacteria, quorum sensing can be inhibited by not allowing the gram negative autoinducers to bind to the LuxR type receptor proteins. This can be done through competitive inhibition when isomers or chemically different molecules that are similar to AHLs bind to the receptors and prevent autoinducers from binding to the LuxR protein. A well known set of chemicals that do this are called furanones. Also, furanones are also responsible for breaking down the LuxR protein and decreasing the binding activity of the transcriptional regulator protein LuxR to DNA in some cases. By taking an AHL and making slight changes to the acyl chain or the lactone ring, the molecule produced can still bind to the LuxR protein but not cause the receptor to activate and send signals downstream through phosphorylation.
Disabling the autoinducer synthase: In gram negative bacteria, one can suppress the production of AHL in gram negative bacteria by creating structural analogs of S-adenosylmethionine and the acyl carrier protein. Some examples are S-adenosylhomocysteine and sinefungin. When these chemicals block off the AHL synthase, no autoinducers can be produced and as a result, the bacteria can not produce the appropriate output for the input signals. Some scientists have researched on antibiotics that can inhibit quorum sensing. It is known that macrolide antibiotics can inhibit the AHL synthase when used at lower concentrations.
In Gram Positive Bacteria:A lot of gram positive research has gone into Staphylococcus aureus because of the extensive damage it is able to do. S. aureus and its quorum sensing will be on the of the main focuses in the following few passage on how to inhibit quorum sensing. Quorum sensing in gram positive bacteria starts with the autoinducers. AIPs in the environment are sensed by two component sensor kinases. When the AIP binds to this, the kinase auto-phosphorylates by passing a phosphoryl group from histidine to an aspartate on a response regulator protein. This results in the response regulator altering the genes targeted by quorum sensing
Disabling the Autoinducer: AIPs are autoinducers that are two to twenty amino acids long. AIPs can be inactivated when the C-terminal methionine of the peptides are oxidized. However, this does not shut off all AIPs because not all autoinducers have a methionine residue. Scientists have been looking into antibodies that can bind to the designated autoinducer to prevent it from binding it to the receptor. An example is an antibody called AP4-24H11 that can bind to AIP-IV in Staphylococcus aureus.
Blocking the receptor: Similarly to quorum quenching in gram negative bacteria, we can block off histidine kinase receptors with the AIP's analog. In S. aureus, Solonamide A and B are known inhibitors that interact with the cytoplasmic membrane and affect AIP-AgrC receptor interaction, which is a transcription factor
Not allowing regulators bind to DNA: Scientists have found ways to disrupt bacteria signaling cascades, specifically blocking transcription factors from binding to the promoter region on DNA. A good example is with Staphylococcus aureus, a species of virulent bacteria known for toxic shock syndrome and sepsis. A molecule called savirin is known to inhibit quorum sensing by binding to AgrA, a transcription factor that regulates virulence and toxin gene expression. This inhibitor was specific to AgrA in S. aureus and so did not affect gene expression in any other good bacteria.
The quorum sensing circuit in a gram positive bacteria Interspecies Communication: The autoinducer and autoinducer synthase for interspecies communication is AI2 and LuxS, respectively. Some bacteria can't get a task done with just its own species - sometimes, it needs help from other bacteria species to achieve a task. Dental plaque is controlled by S. gordonii while peridontal disease is controlled by P. ginivalis. If neither bacteria has a working copy of the LuxS gene, no autoinducers can be produced and so the two bacteria can't create a biofilm. If one has a working copy of the LuxS gene, the biofilim is created because autoinducers can be produced. Inhibiting interspecies communication can be a bit easier because one molecule can knock out all the autoinducers or receptors, but with the drawback of not knowing if it will be beneficial or deleterious. Furanones are known also for inhibiting interspecies communication by covalently modifying and inactivating LuxS, the AI2 autoinducer synthase.
How do we get all these chemicals?: It turns out, bacteria themselves are able to produce these quorum quenching chemicals. It is known that because bacteria are competing for the same resources, they do not always want to help one another out. For example, in the coral environment, dominant bacteria communities are known to secrete various quorum quenching chemicals that will be able to eliminate unwanted bacteria species. By doing this, the dominant bacteria eliminates the prospect of allowing other bacteria to make a biofilm.
Some Problems for Research in the Future: Even though quorum quenching seems has a lot of potential, there are some drawbacks. Quorum quenching may lead to bacterial evolution indirectly. When a bacteria colony creates a biofilm, the quorum quenching molecule has to be able to penetrate this biofilm. Bacteria might be able to resist this by creating extracellular particles that will prevent the quorum quenching molecule from entering. Even though quorum quenching has little selective pressure, it may accidentally select virulent bacteria with the best quorum sensing systems. By quorum quenching, bacteria with weaker systems will be eliminated and only the bacteria with the strongest systems will survive. In the long run, bacteria might be able to create quorum sensing systems different from the ones studied today because of quorum quenching.
Conclusion: By disabling one of these functions, bacteria can’t communicate with each other and cannot express any virulence factors. By using antibiotics to target quorum sensing, bacteria will not evolve because quorum quenching does not cause bacterial genetic information to randomly mutate and not kill bacteria. Quorum quenching will be extremely useful in the future when bacteria get more and more resistant to different types of antibiotics that are being overused as it will be one of our ways to help fight off bacterial infections.
Introduction:
Hi, my name is Brandon Zhang and I'm 15 years old. I'm from Winchester, MA, a small suburb of Boston and I'll be going into 10th grade. I've just finished the beginning chapter of my high school career and look forward to how my knowledge and studies can expand as I travel through high school. Ever since biology was introduced to me in the beginning of my freshmen year, I have always loved it. To this day, it has been my favorite subject in science and I've been particularly interested in biotechnology, microorganisms, and anatomy and physiology.Even though I like traveling and have visited many different cities across the world, I have lived in the Boston area all my life and have been grateful for fifteen years for living in one of the biggest science centers in the United States. The atmosphere that I have been able to be surrounded in is just incredible. The amount of technology being developed here as a result of research in the different fields of science has always amazed me. In addition, the fact that both my parents have worked at Massachusetts General Hospital, one of the top hospitals in the nation for a long time, has piqued my interest in the field of biotechnology and anatomy and physiology. Both my mother and my father has manipulated bacteria and viruses to try to help in the fight with various diseases.
When I am not reading biology articles or thinking about bacteria, I enjoy playing tennis on my high school's varsity team and solving competitive math problems, hobbies of mine since sixth grade. I also have been playing piano for eleven years (I especially love Chopin) and saxophone for four years. Even though getting a concussion from sailing was a painful experience, it was actually a fun one for me because I got to learn a lot about how the brain works and how to protect it in the future.
Just like the elegant proofs to many math problems I have solved over my competitive math career, the beautiful solutions to many real world problems biologist come up has never ceased to amaze me. I would have never of thought of to use electrical currents to separate different lengths of DNA or that DNA comes in a double helix shape with certain rules on how nucleotides pair up. In the mathematics field, you can't just prove the Cauchy-Schwarz inequality when you just get started, but over several weeks, you can develop your skill and knowledge - and that's why I am here at BLI, to develop and improve my biology experimental skills and knowledge of real life problems.
I am looking forward to perform experiments, research on current biology topics and problems, and learn as much as I can about biology at Boston Leadership Institute.
The Future of Antibiotics with Quorum Quenching
Link to the Powerpoint Presentation:
https://docs.google.com/presentation/d/1H0ysKExKyNXAc_yy1tcss1qMl3Ccq4lkeLRkbRrbIb4/edit#slide=id.g116a078e5e_0_62
The Problem: Even though bacteria are microscopic, how are they able to create so much trouble in hosts that are one million times their size? It turns out that bacteria are able to communicate with each other through a method called quorum sensing. With quorum sensing, the bacteria are able to sense how many other bacteria of the same species are in the area. When the concentration of a species reaches a threshold, they can all perform an action simultaneously that will achieve a big task. Virulent bacteria uses this method to talk and organize a gang attack to cause a disruptence in the host organism. With the increased use of antibiotics used to fight off infections, bacteria are starting to evolve to be resistant to antibiotics.History of Quorum Sensing Discoveries: In the late 1960’s, J Woodland Hastings and Kenneth Nealson were studying Vibrio Fischeri, a bacteria that is able to produce light. They realized that the bacteria glows only when high concentrations of them are present. At first, it was believed that in the lower densities of bacteria, there was an inhibitor that prevented light production. However, they eventually realized light production was because of an activator molecule. In 1981, the autoinducer in Vibrio fischeri was discovered by Eberhard. In the early 1990’s, Barrie Bycroft and Paul Williams realized that quorum sensing is not only limited to marine bioluminescent bacteria and that virulent bacterial species use quorum sensing. In 1993, the first biosensers that can detect AHL (an autoinducer that will be discussed later) were developed. Now in modern times, Bonnie Bassler discovered the autoinducer for interspecies communication as well as some molecules that can inhibit quorum sensing and with ideas about if quorum sensing is the link between unicellular organisms and multi-cellular organisms. .
Quorum Sensing in a Nutshell: Bacteria can communicate through quorum sensing by releasing a small protein called an autoinducer. When the autoinducers bind to receptors on the cell membrane the receptors, the bacteria will start producing autoinducers. When these autoinducers reach a certain threshold, the receptors will alter the gene expression directly or indirectly. These receptors directly alters the gene by acting as an activator or repressor to turn genes on or off in gram negative bacteria. They alter the gene indirectly by allowing response regulators to send signals downstream to transcription factors to turn the gene on or off in gram positive bacteria. The altered gene allows bacteria to know that they are in a densely populated area of bacteria and will perform a task that can only be achieved when many bacteria are in the area. By being able to perform quorum sensing, bacteria can maximize its energy output to perform large tasks.
Different types of Quorum Sensing: Bacteria can be classified into two categories based on their cell wall. If bacteria had a thick layer of peptidoglycan in its cell wall, it is classified as gram positive. If bacteria had a thin layer of peptidoglycan in its cell wall, it is classified as gram negative. In gram negative bacteria, quorum sensing is done through three components, the I synthase protein used to make autoinducers, the N-acyl homoserine lactone (AHL) autoinducer, and the R receptor proteins, which are DNA binding transcription factor. AHLs are small neutral lipid molecules made up of a homoserine ring and an acyl chain. The acyl chain is what distinguishes between different types of gram negative bacteria. In gram positive bacteria, quorum sensing is done through a two component signaling system and some response regulators downstream. The two component signaling transduction system uses autoinducing peptides (AIP) as autoinducers and specific histidine kinase receptors that will phosphorylate downstream adaptor proteins once bound. AIPs are different from AHLs because they require cell surface oligopeptides transporters to help AIP secretion into the environment and they are peptides compared to lipids . Below will be a more in depth analysis of quorum sensing in gram negative bacteria versus gram positive bacteria.
Solution: With all the antibiotics being used to fight off infections, targeted bacteria are going to evolve because of the selective pressure of the antibiotics. For quorum sensing to work, all parts of the system have to work. That means scientists can target one of the parts in the quorum sensing system to disable quorum sensing regulated genes and not allow bacteria to express virulence factors. This is known as quorum quenching. Because bacteria usually attacks with its own species and not with others, most of the following solutions will focus on intraspecies communication.
Interspecies Communication: The autoinducer and autoinducer synthase for interspecies communication is AI2 and LuxS, respectively. Some bacteria can't get a task done with just its own species - sometimes, it needs help from other bacteria species to achieve a task. Dental plaque is controlled by S. gordonii while peridontal disease is controlled by P. ginivalis. If neither bacteria has a working copy of the LuxS gene, no autoinducers can be produced and so the two bacteria can't create a biofilm. If one has a working copy of the LuxS gene, the biofilim is created because autoinducers can be produced. Inhibiting interspecies communication can be a bit easier because one molecule can knock out all the autoinducers or receptors, but with the drawback of not knowing if it will be beneficial or deleterious. Furanones are known also for inhibiting interspecies communication by covalently modifying and inactivating LuxS, the AI2 autoinducer synthase.
How do we get all these chemicals?: It turns out, bacteria themselves are able to produce these quorum quenching chemicals. It is known that because bacteria are competing for the same resources, they do not always want to help one another out. For example, in the coral environment, dominant bacteria communities are known to secrete various quorum quenching chemicals that will be able to eliminate unwanted bacteria species. By doing this, the dominant bacteria eliminates the prospect of allowing other bacteria to make a biofilm.
Some Problems for Research in the Future: Even though quorum quenching seems has a lot of potential, there are some drawbacks. Quorum quenching may lead to bacterial evolution indirectly. When a bacteria colony creates a biofilm, the quorum quenching molecule has to be able to penetrate this biofilm. Bacteria might be able to resist this by creating extracellular particles that will prevent the quorum quenching molecule from entering. Even though quorum quenching has little selective pressure, it may accidentally select virulent bacteria with the best quorum sensing systems. By quorum quenching, bacteria with weaker systems will be eliminated and only the bacteria with the strongest systems will survive. In the long run, bacteria might be able to create quorum sensing systems different from the ones studied today because of quorum quenching.
Conclusion: By disabling one of these functions, bacteria can’t communicate with each other and cannot express any virulence factors. By using antibiotics to target quorum sensing, bacteria will not evolve because quorum quenching does not cause bacterial genetic information to randomly mutate and not kill bacteria. Quorum quenching will be extremely useful in the future when bacteria get more and more resistant to different types of antibiotics that are being overused as it will be one of our ways to help fight off bacterial infections.